‘Fatwa’ by the rebel leader against policemen, leads to the death of a police officer’s son who was injured by a fall. In his zeal to wipeout the responsible terrorist leader the police officer ends up killing an entire family of civilians. The only escapee was the ten year old son of the family, who saw the destruction of his entire world by a masked man. The traumatised youth was ultimately adopted by the police officer. The boy finds out by chance that the masked man was his adopted father and runs away. The story of Mission Kashmir is based on the vengeance of the boy.Ten years later ,the rebel boy (Hrithik Roshan) reappears on scene, directed by the rebel leader Hilal Koshistani (Jackie Shroff) sowing seeds of destruction and murder all around. The script takes a turn, when the bomb planted by Altaaf (Hrithik Roshan) meant for the police commissioner (Sanjay Dutt) kills his wife instead. The distraught youth is consoled by his childhood sweet heart Zufi (Preity Zinta) who was working as an anchor at the local TV station. Rest of the movie is when the police commissioner abort the attempt by the rebels to blow up the places of worship.